Simple examples

Install a genome

Any genome on UCSC, Ensembl or NCBI can be installed automatically using genomepy. The genomepy command tool comes installed with gimmemotifs. For instance, to download the hg38 genome from UCSC:

$ genomepy install hg38 UCSC --annotation

Predict de novo motifs

For a quick analysis, to see if it works:

$ gimme motifs TAp73alpha.bed -g hg19 -n gimme.p73 -a small -t Homer,MDmodule,BioProspector

For a full analysis:

$ gimme motifs TAp73alpha.bed -g hg19 -n gimme.p73

Open the file gimme.p73/gimme.denovo.html in your web browser to see the results.

Compare motifs between data sets

$ gimme maelstrom hg19.blood.most_variable.1k.txt hg19 maelstrom.out/

The output scores of gimme maelstrom represent the combined result of multiple methods. The individual results from different methods are ranked from high-scoring motif to low-scoring motif and converted to z-scores using the inverse normal transformation. The z-scores from individual methods are then combined using Stouffer’s method. The score that is shown is the aggregated z-score. A higher z-score means that presence of the motif or a higher motif score is associated with higher signal in a specific sample.

Create sequence logos

$ gimme logo -i GM.5.0.p53.0004

This will generate GM.5.0.p53.0004.png.

_images/GM.5.0.p53.0004.png

Use the -p argument for a different pwm file. The following command will generate a logo for every motif in custom.pfm.

$ gimme logo -p custom.pfm